BRIEF SUMMARY OF THE PIG GENOME COORDINATION PROGRAM FOR 2002

Max F. Rothschild, USDA/CSREES Pig Genome Coordinator

Coordination Structure: A number of faculty members and support staff are participating in the national pig genome coordination effort as part of Iowa State University’s contribution to the project. Dr. Y. Zhang resigned his position to take a faculty position in Australia. Dr. Zhiliang Hu, who had been in this post several years ago, has resumed his outstanding efforts as assistant to the Coordinator.

Map Development Update: New gene markers continue to be identified and mapped and some integration of the maps continues to have taken place as QTL maps are expanded. However, no new large-scale maps have been published recently. In total there are over 924 genes and 1,641 markers in the database. There is a developing AFLP map with about 3,000 AFLPs that is likely to be added to the PiGMaP linkage map some time in the future. The physical map is also growing quickly and there are now nearly 1,315 genes and anonymous markers thanks to a very useful somatic cell hybrid panel and a radiation hybrid panel (RHP) from France. The RHP is available now and being shared.

QTLs and Candidate Genes: QTL have continued to be reported on nearly all chromosomes for growth, carcass and meat quality traits and several chromosomes for reproduction. Some extensive QTL papers have just been published including new ones for meat quality [see review, Bidanel and Rothschild (2002) Pig News and Information]. QTL studies to find imprinted genes continue to grow. Candidate gene analyses have proved successful with several gene tests being used in the industry for stress susceptibility, fat, feed intake, growth, meat quality, litter size and coat color.

Sequencing Efforts: A "White Paper" was submitted to NHGRI recently. Thanks to the efforts of Gary Rohrer, USDA-ARS, US Meat Animal Research Center; Jonathan E. Beever, University of Illinois; Max F. Rothschild, Iowa State University; Larry Schook (corresponding author) University of Illinois; and Richard Gibbs and George Weinstock, Baylor College of Medicine, Human Genome Sequencing Center. The "White Paper" is now being considered and will hopefully obtain "high priority ranking." In addition to the efforts of the authors, the White Paper received solid backing from our colleagues abroad in Denmark, China, Scotland and France and solid support from industry personnel from many companies and organizations. We thank each of them for their support.

Database Activities: As in past years the Pig Genome Database has received considerable updating and a great deal of new information on the maps and mapping tools have been added. There are over 1,093 citations in the database on about 2,565 loci, over 602 clone entries and 96 library entries. Entry to the database can be made at http://www.genome.iastate.edu through the US Pig Genome Coordination home page. This last year the US Pig Genome database had over 84,000 users making 1.4 million hits. In addition, a new EST database (http://pigest.genome.iastate.edu) has been developed and should be a useful resource. It is now in use and contains over 98,988 pig EST entries and further development will continue.

Shared Materials: Thanks to some real partnering with Dr. Pieter de Jong, Children's Hospital Oakland Research Institute and interested labs, the new porcine BAC library and filters were shared among 12 swine genomics labs in the US. A second major project has been the negotiations with companies and other concerns about a pig gene array. We continue to make progress on this and hope to have such an array available by mid year 2003. As in the past primers for three types of microsatellite typing systems were also provided. A total of 559 fluorescent primer pairs covering the entire porcine genome, have now been produced for fluorescent typing and have been shared in over 40 labs world wide. Supplies have been exhausted and are no longer available. Funding for primers for 120 microsatellites have also been made for another typing system. For gene expression, 30 dd-PCR primers have been made. The U.S. reference family DNA is available from Iowa State University and USDA-MARC. PiGMaP family DNA can be shared also. We continue to help other labs wishing to get these needed resources and to develop new ones. We are working to develop new EST resources for the gene mapping community.

International Efforts: Communication with all international groups and individuals is excellent.

Communication: The Pig Genome Update has now published 58 issues bimonthly and has been distributed by mail to over 110 people and electronically to nearly 900 people worldwide. Angenmap, the gene mapping discussion group continues to grow in activity and members. The current list of subscribers has over 900 users from over 40 countries. The address is angenmap@db.genome.iastate.edu.

Travel and Meeting Support: Some conferences have received support funding from the Coordinator. Travel of several scientists was partially funded to attend important pig gene mapping meetings.

Future Activities: Constructive suggestions from researchers to help this coordination and facilitation program grow and succeed are appreciated.